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2014-06-09	Berk Hess	Set make_ndx max name length and count to 1024	commit \| commitdiff \| tree
2014-06-05	Berk Hess	Fix constraint virial with multiple time stepping	commit \| commitdiff \| tree
2014-06-02	Berk Hess	Fixed g_energy Einstein viscosity	commit \| commitdiff \| tree
2014-05-22	Berk Hess	Avoid energy drift with verlet-buffer-tolerance	commit \| commitdiff \| tree
2014-05-09	Berk Hess	Minor tweaks to the DD setup	commit \| commitdiff \| tree
2014-04-29	Berk Hess	Removed truncation of nrdf in v-rescale thermostat	commit \| commitdiff \| tree
2014-04-23	Berk Hess	Fixed nbnxn FE list allocation issue	commit \| commitdiff \| tree
2014-04-02	Berk Hess	Added LJ-PME and LJ Pot-switch to PME load estimate	commit \| commitdiff \| tree
2014-03-24	Berk Hess	Adds cut-off checks for triclinic domain decomposition	commit \| commitdiff \| tree
2014-03-23	Berk Hess	Fixed bug in parallel v/f constraining	commit \| commitdiff \| tree
2014-03-23	Berk Hess	CUDA cut-off kernels now shift exclusion energies	commit \| commitdiff \| tree
2014-03-11	Berk Hess	PME load balancing now works with LJ-PME	commit \| commitdiff \| tree
2014-03-06	Berk Hess	Fixed exit with FEP with PME nodes without LJ-PME	commit \| commitdiff \| tree
2014-03-05	Berk Hess	Buffer estimate now works with rvd-switch=0	commit \| commitdiff \| tree
2014-02-26	Berk Hess	Free-energy now works with the Verlet scheme	commit \| commitdiff \| tree
2014-02-25	Berk Hess	Fixes seperate PME nodes without LJ-PME	commit \| commitdiff \| tree
2014-02-24	Berk Hess	Implemented LJ-PME nbnxn kernels	commit \| commitdiff \| tree
2014-02-24	Berk Hess	Fixed bug with LJ pot-switch in 4xN kernels	commit \| commitdiff \| tree
2014-02-19	Berk Hess	Implemented nbnxn LJ switch functions	commit \| commitdiff \| tree
2014-01-30	Berk Hess	Made reference SIMD work again	commit \| commitdiff \| tree
2014-01-29	Berk Hess	Automated Verlet rlist for NVE simulations	commit \| commitdiff \| tree
2013-12-03	Berk Hess	Removed restriction of one reference pull group	commit \| commitdiff \| tree
2013-12-02	Berk Hess	Made cutoff-scheme=Verlet the default	commit \| commitdiff \| tree
2013-12-02	Berk Hess	Renamed verlet-buffer-drift to verlet-buffer-tolerance	commit \| commitdiff \| tree
2013-12-01	Berk Hess	Fixed zero hardware thread count	commit \| commitdiff \| tree
2013-11-29	Berk Hess	Created SIMD module	commit \| commitdiff \| tree
2013-11-26	Berk Hess	Fixed return value of gmx_mtop_bondeds_free_energy	commit \| commitdiff \| tree
2013-11-15	Berk Hess	corrected potential nbnxn SIMD memory issue	commit \| commitdiff \| tree
2013-11-08	Berk Hess	fix nbnxn atom sorting with distant bondeds	commit \| commitdiff \| tree
2013-11-07	Berk Hess	corrected dynamic load balancing when sharing GPUs	commit \| commitdiff \| tree
2013-11-05	Berk Hess	GPU detection is done once per physical node	commit \| commitdiff \| tree
2013-11-05	Berk Hess	removed (harmless) left-over in nbnxn SIMD kernels	commit \| commitdiff \| tree
2013-10-31	Berk Hess	reorganized GPU detection and selection	commit \| commitdiff \| tree
2013-10-29	Berk Hess	corrected volume with serial NPT replica exchange	commit \| commitdiff \| tree
2013-10-28	Berk Hess	improved the nbnxn buffer size estimate with GPUs	commit \| commitdiff \| tree
2013-10-22	Berk Hess	fixed recent bug with CUDA texture objects	commit \| commitdiff \| tree
2013-10-22	Berk Hess	fixed OpenMP threads being pinned to the same cores	commit \| commitdiff \| tree
2013-10-16	Berk Hess	avoid division by zero in SIMD angles and dihedrals	commit \| commitdiff \| tree
2013-10-16	Berk Hess	fixed a half bin misalignment in gmx_vanhove -or	commit \| commitdiff \| tree
2013-10-11	Berk Hess	introduced general 4-wide SIMD support	commit \| commitdiff \| tree
2013-10-10	Berk Hess	fixed nbnxn 4x8 pair search without AVX	commit \| commitdiff \| tree
2013-10-02	Berk Hess	Fixes reaction field free energy bug	commit \| commitdiff \| tree
2013-09-24	Berk Hess	optimized generic SIMD invsqrt	commit \| commitdiff \| tree
2013-09-21	Berk Hess	fixed multiple distance restraints with OpenMP	commit \| commitdiff \| tree
2013-09-18	Berk Hess	made free energy PME kernel 40% faster	commit \| commitdiff \| tree
2013-09-16	Berk Hess	mdrun without OpenMP with thread-MPI now uses all cores	commit \| commitdiff \| tree
2013-09-13	Berk Hess	corrected grompp constraint/DOF warning with vsites	commit \| commitdiff \| tree
2013-08-25	Berk Hess	introduced nbnxn data structure for bounding boxes	commit \| commitdiff \| tree
2013-08-20	Berk Hess	fixed parallel normal modes with PME	commit \| commitdiff \| tree
2013-07-24	Berk Hess	implemented plain-C SIMD macros for reference	commit \| commitdiff \| tree
2013-06-20	Berk Hess	fixed SD and BD integrator OpenMP performance	commit \| commitdiff \| tree
2013-06-20	Berk Hess	flops table now reports CUDA analytical Ewald	commit \| commitdiff \| tree
2013-06-14	Berk Hess	fixed minor g_bar output issues	commit \| commitdiff \| tree
2013-06-05	Berk Hess	fixed DD internal state corruption with energy minimization	commit \| commitdiff \| tree
2013-06-03	Berk Hess	fixed deadlock with replica exchange and -maxh	commit \| commitdiff \| tree
2013-05-08	Berk Hess	fixed incorrect scaling of cos-acceleration viscosity	commit \| commitdiff \| tree
2013-04-29	Berk Hess	general SIMD acceleration for angles+dihedrals	commit \| commitdiff \| tree
2013-04-26	Berk Hess	PME load balancing now checks for PME grid restrictions	commit \| commitdiff \| tree
2013-04-18	Berk Hess	changed mdrun -nsteps to gmx_large_int_t	commit \| commitdiff \| tree
2013-04-12	Berk Hess	improved load balancing with Verlet cut-off scheme	commit \| commitdiff \| tree
2013-03-27	Berk Hess	removed x86 specifics from nbnxn SIMD kernels	commit \| commitdiff \| tree
2013-03-27	Berk Hess	corrected log file wall time breakdown	commit \| commitdiff \| tree
2013-03-21	Berk Hess	made PME work with a mix of 1 and more threads	commit \| commitdiff \| tree
2013-03-14	Berk Hess	corrected grompp rvdw charge-group radii check	commit \| commitdiff \| tree
2013-03-05	Berk Hess	fixed bug with DD cut-off check and PME DLB	commit \| commitdiff \| tree
2013-03-05	Berk Hess	fixed recent bug with sorting atoms for GPUs	commit \| commitdiff \| tree
2013-02-26	Berk Hess	fixed PME time print with -ntomp_pme != -ntomp	commit \| commitdiff \| tree
2013-02-20	Berk Hess	added mdrun check for Verlet+perturbed atoms	commit \| commitdiff \| tree
2013-02-20	Berk Hess	fixed issues with FEP soft-core and cut-off's	commit \| commitdiff \| tree
2013-02-18	Berk Hess	fixed GPU particle gridding performance issue	commit \| commitdiff \| tree
2013-02-15	Berk Hess	improved PME load balancing reporting	commit \| commitdiff \| tree
2013-02-06	Berk Hess	fixed bug with sd integrator and OpenMP threading	commit \| commitdiff \| tree
2013-02-05	Berk Hess	improved load balancing on the GPU	commit \| commitdiff \| tree
2013-02-04	Berk Hess	fixed segv in init_forcerec with fr->hwinfo=NULL	commit \| commitdiff \| tree
2013-02-01	Berk Hess	PME-only counters are now reset with -maxh -resethway	commit \| commitdiff \| tree
2013-01-18	Berk Hess	thread affinity now uses some topology information	commit \| commitdiff \| tree
2013-01-17	Berk Hess	fixed SD+BD integration slowing down with OpenMP threads	commit \| commitdiff \| tree
2013-01-17	Berk Hess	improved CUDA kernel performance by pre-loading cj	commit \| commitdiff \| tree
2013-01-17	Berk Hess	fixed nbnxn hybrid mode with OpenMP	commit \| commitdiff \| tree
2013-01-17	Berk Hess	made PME load balancing + DD DLB more efficient	commit \| commitdiff \| tree
2013-01-16	Berk Hess	split off pick_nbnxn_resource from nbnxn_pick_nbnxn	commit \| commitdiff \| tree
2013-01-13	Berk Hess	fixed resetting states with parallel Verlet scheme	commit \| commitdiff \| tree
2013-01-12	Berk Hess	prepared the nbnxn code for non-x86 SIMD	commit \| commitdiff \| tree
2013-01-11	Berk Hess	made SHAKE work again with particle decompostion	commit \| commitdiff \| tree
2013-01-10	Berk Hess	fixed nbnxn no LJ comb.rule AVX256 PME kernel	commit \| commitdiff \| tree
2013-01-10	Berk Hess	fixed bug with Verlet + DD + bonded atom communication	commit \| commitdiff \| tree
2013-01-07	Berk Hess	fixed nbnxn AVX-256 Ewald table pointer alignment	commit \| commitdiff \| tree
2013-01-02	Berk Hess	minor speed-up and code clean-up in nbnxn kernels	commit \| commitdiff \| tree
2012-12-20	Berk Hess	fixed recent bugs in LINCS for derivatives	commit \| commitdiff \| tree
2012-12-18	Berk Hess	renamed gmx_x86_simd_macros.h to gmx_simd_macros.h	commit \| commitdiff \| tree
2012-12-18	Berk Hess	implemented nbnxn AVX-256 2x(N+N) kernels	commit \| commitdiff \| tree
2012-12-11	Berk Hess	reduced PLINCS communication with H-bond constraints	commit \| commitdiff \| tree
2012-12-07	Berk Hess	fixed GPU pair-search with GMX_CPU_ACCELERATION=None	commit \| commitdiff \| tree
2012-12-06	Berk Hess	removed last OpenMP O(nthreads) bottleneck	commit \| commitdiff \| tree
2012-12-05	Berk Hess	fixed incorrect virial with virtual sites and OpenMP	commit \| commitdiff \| tree
2012-12-05	Berk Hess	fixed segv in Verlet pair-search with trilinic DD	commit \| commitdiff \| tree
2012-11-30	Berk Hess	fixed issue with -multi and GPUs	commit \| commitdiff \| tree
2012-11-28	Berk Hess	fixed thread pinning with mdrun -multi	commit \| commitdiff \| tree
2012-11-28	Berk Hess	extended nbnxn x86 SIMD kernel blendv support	commit \| commitdiff \| tree
2012-11-27	Berk Hess	fixed bug in nbnxn OpenMP non-bonded force reduction	commit \| commitdiff \| tree
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